Calcium in PDB 6oqq: Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex

The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq was solved by D.R.Tomchick, V.S.Tagliabracci, M.Black, A.Osinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.490, 104.749, 107.770, 90.00, 103.97, 90.00
R / Rfree (%)	20.2 / 23.4

The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex (pdb code 6oqq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:55.8 occ:1.00 OD1 B:ASN25 2.2 32.3 1.0 O B:HOH321 2.2 46.0 1.0 OD1 B:ASP23 2.3 43.0 1.0 O B:SER27 2.3 27.4 1.0 OD1 B:ASP21 2.4 26.5 1.0 CG B:ASN25 2.9 31.8 1.0 H B:ASN25 3.0 31.2 1.0 H B:SER27 3.1 31.0 1.0 HD21 B:ASN25 3.2 47.6 1.0 ND2 B:ASN25 3.4 39.6 1.0 CG B:ASP23 3.4 29.2 1.0 CG B:ASP21 3.5 26.2 1.0 C B:SER27 3.5 26.9 1.0 HG B:SER27 3.6 36.8 1.0 H B:ASP23 3.7 65.6 1.0 N B:ASN25 3.8 26.1 1.0 H B:ASN24 3.8 42.1 1.0 HA B:ASP21 3.8 32.8 1.0 OD2 B:ASP23 3.9 41.0 1.0 N B:SER27 3.9 26.0 1.0 HA B:ILE28 4.0 33.7 1.0 CB B:ASN25 4.1 26.7 1.0 OG B:SER27 4.1 30.6 1.0 H B:GLY26 4.1 30.3 1.0 HD22 B:ASN25 4.1 47.6 1.0 N B:ASN24 4.2 35.0 1.0 OE1 B:GLN63 4.2 73.8 1.0 OD2 B:ASP21 4.2 25.9 1.0 CA B:SER27 4.3 26.7 1.0 HB3 B:ASN25 4.3 31.9 1.0 CA B:ASN25 4.3 25.9 1.0 N B:ASP23 4.4 54.6 1.0 H B:LYS22 4.4 79.3 1.0 CA B:ASP21 4.4 27.4 1.0 CB B:ASP21 4.4 26.7 1.0 N B:GLY26 4.5 25.4 1.0 N B:ILE28 4.6 47.9 1.0 C B:ASP21 4.6 28.1 1.0 C B:ASP23 4.6 28.4 1.0 N B:LYS22 4.6 66.0 1.0 C B:ASN25 4.6 25.6 1.0 HB2 B:ASP21 4.7 31.9 1.0 O B:HOH327 4.7 47.5 1.0 CB B:ASP23 4.7 37.6 1.0 CA B:ILE28 4.8 28.2 1.0 CA B:ASP23 4.8 39.8 1.0 HA B:ASN24 4.8 32.9 1.0 C B:ASN24 4.8 26.8 1.0 CB B:SER27 4.8 27.5 1.0 CA B:ASN24 4.9 27.4 1.0 HB2 B:ASN25 4.9 31.9 1.0

Calcium binding site 2 out of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:0.8 occ:1.00 OD1 B:ASP94 2.3 63.6 1.0 OD1 B:ASN96 2.4 97.5 1.0 O B:LEU100 2.4 64.7 1.0 OD1 B:ASP98 2.6 78.5 1.0 CG B:ASN96 3.2 0.3 1.0 HA B:ASP94 3.4 73.4 1.0 CG B:ASP98 3.4 79.4 1.0 CG B:ASP94 3.5 77.7 1.0 HD21 B:ASN96 3.6 0.5 1.0 H B:ASP98 3.7 98.5 1.0 C B:LEU100 3.7 66.0 1.0 H B:LEU100 3.7 76.8 1.0 OD2 B:ASP98 3.7 80.1 1.0 H B:ASN96 3.7 0.0 1.0 ND2 B:ASN96 3.8 94.6 1.0 H B:GLY97 3.9 0.3 1.0 HA B:ILE101 3.9 92.3 1.0 CA B:ASP94 4.1 61.1 1.0 H B:LYS95 4.1 0.9 1.0 CB B:ASP94 4.1 63.9 1.0 HB2 B:ASP94 4.1 76.7 1.0 HB2 B:LEU100 4.2 84.6 1.0 HB3 B:ASN96 4.3 0.4 1.0 CB B:ASN96 4.3 97.0 1.0 N B:LEU100 4.3 64.0 1.0 N B:ASN96 4.4 86.7 1.0 N B:ASP98 4.4 82.0 1.0 N B:LYS95 4.5 89.9 1.0 OD2 B:ASP94 4.5 72.6 1.0 CA B:LEU100 4.5 66.4 1.0 N B:GLY97 4.5 91.1 1.0 H B:GLY99 4.5 84.5 1.0 C B:ASP94 4.5 65.6 1.0 HD22 B:ASN96 4.6 0.5 1.0 CB B:ASP98 4.6 81.9 1.0 N B:ILE101 4.6 72.2 1.0 HB3 B:ASP98 4.7 98.4 1.0 CA B:ILE101 4.7 76.9 1.0 CA B:ASN96 4.8 98.3 1.0 CB B:LEU100 4.8 70.5 1.0 HG23 B:ILE101 5.0 75.3 1.0 N B:GLY99 5.0 70.3 1.0

Calcium binding site 3 out of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:81.5 occ:1.00 O D:SER27 2.2 69.2 1.0 OD1 D:ASP23 2.3 77.4 1.0 OD1 D:ASN25 2.6 60.0 1.0 OD1 D:ASP21 2.6 59.6 1.0 HD21 D:ASN25 2.9 78.7 1.0 CG D:ASP23 3.2 68.5 1.0 CG D:ASN25 3.2 60.2 1.0 H D:SER27 3.2 73.3 1.0 ND2 D:ASN25 3.3 65.5 1.0 C D:SER27 3.3 62.3 1.0 OD2 D:ASP23 3.4 72.9 1.0 HG D:SER27 3.5 83.5 1.0 HA D:ASP21 3.6 71.4 1.0 H D:ASN25 3.7 71.2 1.0 HA D:ILE28 3.7 90.0 1.0 CG D:ASP21 3.7 59.4 1.0 H D:ASP23 3.9 75.5 1.0 OG D:SER27 4.0 69.5 1.0 N D:SER27 4.0 61.1 1.0 HD22 D:ASN25 4.1 78.7 1.0 CA D:SER27 4.2 60.3 1.0 N D:ILE28 4.3 89.2 1.0 CA D:ASP21 4.3 59.6 1.0 H D:ASN24 4.4 71.6 1.0 H D:GLY26 4.4 70.9 1.0 CA D:ILE28 4.4 75.0 1.0 N D:ASN25 4.4 59.4 1.0 CB D:ASP21 4.4 59.4 1.0 HB2 D:ASP21 4.5 71.1 1.0 CB D:ASN25 4.5 60.6 1.0 HG2 D:GLN63 4.5 0.1 1.0 CB D:ASP23 4.5 62.6 1.0 OD2 D:ASP21 4.6 59.1 1.0 H D:SER29 4.6 79.9 1.0 H D:LYS22 4.6 0.8 1.0 N D:ASP23 4.7 62.9 1.0 CB D:SER27 4.7 60.8 1.0 HB3 D:ASN25 4.7 72.7 1.0 C D:ASP21 4.8 59.8 1.0 N D:GLY26 4.8 59.2 1.0 N D:ASN24 4.8 59.8 1.0 C D:ILE28 4.8 81.4 1.0 HB3 D:ASP23 4.8 75.2 1.0 N D:LYS22 4.9 89.8 1.0 N D:SER29 4.9 66.6 1.0 CA D:ASN25 4.9 59.4 1.0

Calcium binding site 4 out of 4 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:0.6 occ:1.00 HD21 D:ASN96 1.9 0.7 1.0 OD1 D:ASN96 2.4 0.7 1.0 ND2 D:ASN96 2.4 0.5 1.0 OD1 D:ASP94 2.6 89.5 1.0 O D:LEU100 2.6 91.3 1.0 OD1 D:ASP98 2.7 0.1 1.0 CG D:ASN96 2.7 0.3 1.0 OD2 D:ASP98 2.9 0.8 1.0 CG D:ASP98 3.0 0.5 1.0 HD22 D:ASN96 3.2 0.7 1.0 H D:ASN96 3.6 0.7 1.0 H D:ASP98 3.6 0.9 1.0 H D:LEU100 3.7 0.7 1.0 CG D:ASP94 3.7 90.3 1.0 HB3 D:LEU100 3.7 0.4 1.0 H D:GLY97 3.8 0.9 1.0 C D:LEU100 3.8 96.2 1.0 HA D:ASP94 3.9 0.2 1.0 CB D:ASN96 4.2 0.4 1.0 H D:LYS95 4.3 0.8 1.0 CB D:ASP98 4.3 0.4 1.0 N D:LEU100 4.3 0.1 1.0 HA D:ILE101 4.3 0.2 1.0 N D:ASN96 4.4 0.6 1.0 N D:ASP98 4.4 0.1 1.0 OD2 D:ASP94 4.4 88.1 1.0 CA D:LEU100 4.4 0.7 1.0 HB3 D:ASN96 4.5 0.9 1.0 HB3 D:ASP98 4.5 0.5 1.0 CB D:LEU100 4.5 97.8 1.0 H D:GLY99 4.5 0.4 1.0 N D:GLY97 4.5 0.5 1.0 CA D:ASP94 4.6 91.8 1.0 HG22 D:ILE101 4.6 99.8 1.0 CB D:ASP94 4.6 93.8 1.0 N D:LYS95 4.7 0.9 1.0 HD23 D:LEU100 4.7 0.4 1.0 HB2 D:ASN96 4.7 0.9 1.0 CA D:ASN96 4.8 0.6 1.0 C D:ASP94 4.8 85.1 1.0 N D:ILE101 4.8 93.8 1.0 HB2 D:ASP94 4.9 0.6 1.0 CA D:ASP98 4.9 0.8 1.0 N D:GLY99 5.0 0.3 1.0

M.H.Black, A.Osinski, M.Gradowski, K.A.Servage, K.Pawlowski, D.R.Tomchick, V.S.Tagliabracci. Bacterial Pseudokinase Catalyzes Protein Polyglutamylation to Inhibit the Side-Family Ubiquitin Ligases. Science V. 364 787 2019.
ISSN: ESSN 1095-9203
PubMed: 31123136
DOI: 10.1126/SCIENCE.AAW7446